Colorectal cancer is the second leading cause of cancer-related deaths behind lung cancer in the United States. Colonoscopy is the preferred screening method for detection of diseases like Colorectal Cancer. In the year 2006, American Society for Gastrointestinal Endoscopy (ASGE) and American College of Gastroenterology (ACG) issued guidelines for quality colonoscopy. The guidelines suggest that on average the withdrawal phase during a screening colonoscopy should last a minimum of 6 minutes. My aim is to classify the colonoscopy video into insertion and withdrawal phase. The problem is that currently existing shot detection techniques cannot be applied because colonoscopy is a single camera shot from start to end. An algorithm to detect phase boundary has already been developed by the MIGLAB team. Existing method has acceptable levels of accuracy but the main issue is dependency on MPEG (Moving Pictures Expert Group) 1/2. I implemented exhaustive search for motion estimation to reduce the execution time and improve the accuracy. I took advantages of the C/C++ programming languages with multithreading which helped us get even better performances in terms of execution time. I propose a method for improving the current method of colonoscopy video analysis and also an extension for the same to …

Performance and power consumption are most important issues while designing embedded systems. Several studies have shown that cache memory consumes about 50% of the total power in these systems. Thus, the architecture of the cache governs both performance and power usage of embedded systems. A new N-way reconfigurable data cache is proposed especially for embedded systems. This thesis explores the issues and design considerations involved in designing a reconfigurable cache. The proposed reconfigurable data cache architecture can be configured as direct-mapped, two-way, or four-way set associative using a mode selector. The module has been designed and simulated in Xilinx ISE 9.1i and ModelSim SE 6.3e using the Verilog hardware description language.

Non-strict pure functional programming often requires redesigning algorithms and data structures to work more effectively under new constraints of non-strict evaluation and immutable state. Graph drawing algorithms, while numerous and broadly studied, have no presence in the non-strict pure functional programming model. Additionally, there is currently no freely licensed standalone toolkit used to quantitatively analyze aesthetics of graph drawings. This thesis addresses two previously unexplored questions. Can a force-directed graph drawing algorithm be implemented in a non-strict functional language, such as Haskell, and still be practically usable? Can an easily extensible aesthetic measuring tool be implemented in a language such as Haskell and still be practically usable? The focus of the thesis is on implementing one of the simplest force-directed algorithms, that of Fruchterman and Reingold, and comparing its resulting aesthetics to those of a well-known C++ implementation of the same algorithm.

Our generation has experienced one of the most dramatic changes in how society communicates. Today, we have online information on almost any imaginable topic. However, most of this information is available in only a few dozen languages. In this thesis, I explore the use of parallel texts to enable cross-language information retrieval (CLIR) for languages with scarce resources. To build the parallel text I use the Bible. I evaluate different variables and their impact on the resulting CLIR system, specifically: (1) the CLIR results when using different amounts of parallel text; (2) the role of paraphrasing on the quality of the CLIR output; (3) the impact on accuracy when translating the query versus translating the collection of documents; and finally (4) how the results are affected by the use of different dialects. The results show that all these variables have a direct impact on the quality of the CLIR system.

In this thesis, I survey 11 approximation algorithms for unweighted set cover problem. I have also implemented the three algorithms and created a software library that stores the code I have written. The algorithms I survey are: 1. Johnson's standard greedy; 2. f-frequency greedy; 3. Goldsmidt, Hochbaum and Yu's modified greedy; 4. Halldorsson's local optimization; 5. Dur and Furer semi local optimization; 6. Asaf Levin's improvement to Dur and Furer; 7. Simple rounding; 8. Randomized rounding; 9. LP duality; 10. Primal-dual schema; and 11. Network flow technique. Most of the algorithms surveyed are refinements of standard greedy algorithm.

Environmental monitoring represents a major application domain for wireless sensor networks (WSN). However, despite significant advances in recent years, there are still many challenging issues to be addressed to exploit the full potential of the emerging WSN technology. In this dissertation, we introduce the design and implementation of low-power wireless sensor networks for long-term, autonomous, and near-real-time environmental monitoring applications. We have developed an out-of-box solution consisting of a suite of software, protocols and algorithms to provide reliable data collection with extremely low power consumption. Two wireless sensor networks based on the proposed solution have been deployed in remote field stations to monitor soil moisture along with other environmental parameters. As parts of the ever-growing environmental monitoring cyberinfrastructure, these networks have been integrated into the Texas Environmental Observatory system for long-term operation. Environmental measurement and network performance results are presented to demonstrate the capability, reliability and energy-efficiency of the network.

The widely used mobile phone, as well as its related technologies had opened opportunities for a complete change on how people interact and build relationship across geographic and time considerations. The convenience of instant communication by mobile phones that broke the barrier of space and time is evidently the key motivational point on why such technologies so important in people's life and daily activities. Mobile phones have become the most popular communication tools. Mobile phone technology is apparently changing our relationship to each other in our work and lives. The impact of new technologies on people's lives in social spaces gives us the chance to rethink the possibilities of technologies in social interaction. Accordingly, mobile phones are basically changing social relations in ways that are intricate to measure with any precision. In this dissertation I propose a socioscope model for social network, relationship and human behavior analysis based on mobile phone call detail records. Because of the diversities and complexities of human social behavior, one technique cannot detect different features of human social behaviors. Therefore I use multiple probability and statistical methods for quantifying social groups, relationships and communication patterns, for predicting social tie strengths and for detecting human behavior …

Researchers have speculated that global software teams have activity patterns that are dictated by work-place schedules or a client's need. Similar patterns have been suggested for individuals enrolled in distant learning projects that require students to post feedback in response to questions or assignments. Researchers tend to accept the notion that students' temporal patterns adjust to academic or social calendars and are a result of choices made within these constraints. Although there is some evidence that culture do have an impact on communication activity behavior, there is not a clear how each of these factors may relate to work done in online groups. This particular study represents a new approach to studying student-group communication activities and also pursues an alternative approach by using activity data from students participating in a global software development project to generate a variety of complex measures that capture patterns about when students work. Students work habits are also often determined by where they live and what they are working on. Moreover, students tend to work on group projects in cycles, which correspond to a start, middle, and end time period. Knowledge obtained from this study should provide insight into current empirical research on global software …

Extracting information from a stack of data is a tedious task and the scenario is no different in proteomics. Volumes of research papers are published about study of various proteins in several species, their interactions with other proteins and identification of protein(s) as possible biomarker in causing diseases. It is a challenging task for biologists to keep track of these developments manually by reading through the literatures. Several tools have been developed by computer linguists to assist identification, extraction and hypotheses generation of proteins and protein-protein interactions from biomedical publications and protein databases. However, they are confronted with the challenges of term variation, term ambiguity, access only to abstracts and inconsistencies in time-consuming manual curation of protein and protein-protein interaction repositories. This work attempts to attenuate the challenges by extracting protein-protein interactions in humans and elicit possible interactions using associative rule mining on full text, abstracts and captions from figures available from publicly available biomedical literature databases. Two such databases are used in our study: Directory of Open Access Journals (DOAJ) and PubMed Central (PMC). A corpus is built using articles based on search terms. A dataset of more than 38,000 protein-protein interactions from the Human Protein Reference Database (HPRD) …

Colonoscopy is an endoscopic technique that allows a physician to inspect the mucosa of the human colon. Previous methods and software solutions to detect informative frames in a colonoscopy video (a process called informative frame filtering or IFF) have been hugely ineffective in (1) covering the proper definition of an informative frame in the broadest sense and (2) striking an optimal balance between accuracy and speed of classification in both real-time and non real-time medical procedures. In my thesis, I propose a more effective method and faster software solutions for IFF which is more effective due to the introduction of a heuristic algorithm (derived from experimental analysis of typical colon features) for classification. It contributed to a 5-10% boost in various performance metrics for IFF. The software modules are faster due to the incorporation of sophisticated parallel-processing oriented coding techniques on modern microprocessors. Two IFF modules were created, one for post-procedure and the other for real-time. Code optimizations through NVIDIA CUDA for GPU processing and/or CPU multi-threading concepts embedded in two significant microprocessor design philosophies (multi-core design and many-core design) resulted a 5-fold acceleration for the post-procedure module and a 40-fold acceleration for the real-time module. Some innovative software modules, …

The fight against epidemics/pandemics is one of man versus nature. Technological advances have not only improved existing methods for monitoring and controlling disease outbreaks, but have also provided new means for investigation, such as through modeling and simulation. This dissertation explores the relationship between social structure and disease dynamics. Social structures are modeled as graphs, and outbreaks are simulated based on a well-recognized standard, the susceptible-infectious-removed (SIR) paradigm. Two independent, but related, studies are presented. The first involves measuring the severity of outbreaks as social network parameters are altered. The second study investigates the efficacy of various vaccination policies based on social structure. Three disease-related centrality measures are introduced, contact, transmission, and spread centrality, which are related to previously established centrality measures degree, betweenness, and closeness, respectively. The results of experiments presented in this dissertation indicate that reducing the neighborhood size along with outside-of-neighborhood contacts diminishes the severity of disease outbreaks. Vaccination strategies can effectively reduce these parameters. Additionally, vaccination policies that target individuals with high centrality are generally shown to be slightly more effective than a random vaccination policy. These results combined with past and future studies will assist public health officials in their effort to minimize the effects …

The presence of naturally occurring and man-made public health threats necessitate the design and implementation of mitigation strategies, such that adequate response is provided in a timely manner. Since multiple variables, such as geographic properties, resource constraints, and government mandated time-frames must be accounted for, computational methods provide the necessary tools to develop contingency response plans while respecting underlying data and assumptions. A typical response scenario involves the placement of points of dispensing (PODs) in the affected geographic region to supply vaccines or medications to the general public. Computational tools aid in the analysis of such response plans, as well as in the strategic placement of PODs, such that feasible response scenarios can be developed. Due to the sensitivity of bio-emergency response plans, geographic information, such as POD locations, must be kept confidential. The generation of synthetic geographic regions allows for the development of emergency response plans on non-sensitive data, as well as for the study of the effects of single geographic parameters. Further, synthetic representations of geographic regions allow for results to be published and evaluated by the scientific community. This dissertation presents methodology for the analysis of bio-emergency response plans, methods for plan optimization, as well as methodology …

Smart phones today have become increasingly popular with the general public for its diverse abilities like navigation, social networking, and multimedia facilities to name a few. These phones are equipped with high end processors, high resolution cameras, built-in sensors like accelerometer, orientation-sensor, light-sensor, and much more. According to comScore survey, 25.3% of US adults use smart phones in their daily lives. Motivated by the capability of smart phones and their extensive usage, I focused on utilizing them for bio-medical applications. In this thesis, I present a new application for a smart phone to quantify the vital signs such as heart rate, respiratory rate and blood pressure with the help of its built-in sensors. Using the camera and a microphone, I have shown how the blood pressure and heart rate can be determined for a subject. People sometimes encounter minor situations like fainting or fatal accidents like car crash at unexpected times and places. It would be useful to have a device which can measure all vital signs in such an event. The second part of this thesis demonstrates a new mode of communication for next generation 9-1-1 calls. In this new architecture, the call-taker will be able to control the …

Wireless sensor networks are composed of sensor nodes, which can monitor an environment and observe events of interest. These networks are applied in various fields including but not limited to environmental, industrial and habitat monitoring. In many applications, the exact location of the sensor nodes is unknown after deployment. Localization is a process used to find sensor node's positional coordinates, which is vital information. The localization is generally assisted by anchor nodes that are also sensor nodes but with known locations. Anchor nodes generally are expensive and need to be optimally placed for effective localization. Passive localization is one of the localization techniques where the sensor nodes silently listen to the global events like thunder sounds, seismic waves, lighting, etc. According to previous studies, the ideal location to place anchor nodes was on the perimeter of the sensor network. This may not be the case in passive localization, since the function of anchor nodes here is different than the anchor nodes used in other localization systems. I do extensive studies on positioning anchor nodes for effective localization. Several simulations are run in dense and sparse networks for proper positioning of anchor nodes. I show that, for effective passive localization, the …

Video surveillance systems have been commonly used in transportation systems to support traffic monitoring, speed estimation, and incident detection. However, there are several challenges in developing and deploying such systems, including high development and maintenance costs, bandwidth bottleneck for long range link, and lack of advanced analytics. In this thesis, I leverage current wireless, video camera, and analytics technologies, and present a wireless traffic monitoring system. I first present an overview of the system. Then I describe the site investigation and several test links with different hardware/software configurations to demonstrate the effectiveness of the system. The system development process was documented to provide guidelines for future development. Furthermore, I propose a novel speed-estimation analytics algorithm that takes into consideration roads with slope angles. I prove the correctness of the algorithm theoretically, and validate the effectiveness of the algorithm experimentally. The experimental results on both synthetic and real dataset show that the algorithm is more accurate than the baseline algorithm 80% of the time. On average the accuracy improvement of speed estimation is over 3.7% even for very small slope angles.

Directly mapped caches are an attractive option for processor designers as they combine fast lookup times with reduced complexity and area. However, directly-mapped caches are prone to higher miss-rates as there are no candidates for replacement on a cache miss, hence data residing in a cache set would have to be evicted to the next level cache. Another issue that inhibits cache performance is the non-uniformity of accesses exhibited by most applications: some sets are under-utilized while others receive the majority of accesses. This implies that increasing the size of caches may not lead to proportionally improved cache hit rates. Several solutions that address cache non-uniformity have been proposed in the literature. These techniques have been proposed over the past decade and each proposal independently claims the benefit of reduced conflict misses. However, because the published results use different benchmarks and different experimental setups, (there is no established frame of reference for comparing these results) it is not easy to compare them. In this work we report a side-by-side comparison of these techniques. Finally, we propose and Adaptive-Partitioned cache for multi-threaded applications. This design limits inter-thread thrashing while dynamically reducing traffic to heavily accessed sets.

Sense amplifiers are important circuit components of a dynamic random access memory (DRAM), which forms the main memory of digital computers. The ability of the sense amplifier to detect and amplify voltage signals to correctly interpret data in DRAM cells cannot be understated. The sense amplifier plays a significant role in the overall speed of the DRAM. Sense amplifiers require matched transistors for optimal performance. Hence, the effects of mismatch through process variations must be minimized. This thesis presents a research which leads to optimal nanoscale CMOS sense amplifiers by incorporating the effects of process variation early in the design process. The effects of process variation on the performance of a standard voltage sense amplifier, which is used in conventional DRAMs, is studied. Parametric analysis is performed through circuit simulations to investigate which parameters have the most impact on the performance of the sense amplifier. The figures-of-merit (FoMs) used to characterize the circuit are the precharge time, power dissipation, sense delay and sense margin. Statistical analysis is also performed to study the impact of process variations on each FoM. By analyzing the results from the statistical study, a method is presented to select parameter values that minimize the effects of …

Embedded systems which are targeted towards portable applications are required to have low power consumption because such portable devices are typically powered by batteries. During the memory accesses of such battery operated portable systems, including laptops, cell phones and other devices, a significant amount of power or energy is consumed which significantly affects the battery life. Therefore, efficient and leakage power saving cache designs are needed for longer operation of battery powered applications. Design engineers have limited control over many design parameters of the circuit and hence face many chal-lenges due to inherent process technology variations, particularly on static random access memory (SRAM) circuit design. As CMOS process technologies scale down deeper into the nanometer regime, the push for high performance and reliable systems becomes even more challenging. As a result, developing low-power designs while maintaining better performance of the circuit becomes a very difficult task. Furthermore, a major need for accurate analysis and optimization of various forms of total power dissipation and performance in nanoscale CMOS technologies, particularly in SRAMs, is another critical issue to be considered. This dissertation proposes power-leakage and static noise margin (SNM) analysis and methodologies to achieve optimized static random access memories (SRAMs). Alternate topologies …

Keyphrases describe a document in a coherent and simple way, giving the prospective reader a way to quickly determine whether the document satisfies their information needs. The pervasion of huge amount of information on Web, with only a small amount of documents have keyphrases extracted, there is a definite need to discover automatic keyphrase extraction systems. Typically, a document written by human develops around one or more general concepts or sub-concepts. These concepts or sub-concepts should be structured and semantically related with each other, so that they can form the meaningful representation of a document. Considering the fact, the phrases or concepts in a document are related to each other, a new approach for keyphrase extraction is introduced that exploits the semantic relations in the document. For measuring the semantic relations between concepts or sub-concepts in the document, I present a comprehensive study aimed at using collaboratively constructed semantic resources like Wikipedia and its link structure. In particular, I introduce a graph-based keyphrase extraction system that exploits the semantic relations in the document and features such as term frequency. I evaluated the proposed system using novel measures and the results obtained compare favorably with previously published results on established benchmarks.

The advent of sensory and communication technologies enables the generation and consumption of large volumes of streaming data. Many of these data streams are geo-referenced. Existing spatio-temporal databases and data stream management systems are not capable of handling real time queries on spatial extents. In this thesis, we investigated several fundamental research issues toward building a data-type-based real time geospatial data stream management system. The thesis makes contributions in the following areas: geo-stream data models, aggregation, window-based nearest neighbor operators, and query optimization strategies. The proposed geo-stream data model is based on second-order logic and multi-typed algebra. Both abstract and discrete data models are proposed and exemplified. I further propose two useful geo-stream operators, namely Region By and WNN, which abstract common aggregation and nearest neighbor queries as generalized data model constructs. Finally, I propose three query optimization algorithms based on spatial, temporal, and spatio-temporal constraints of geo-streams. I show the effectiveness of the data model through many query examples. The effectiveness and the efficiency of the algorithms are validated through extensive experiments on both synthetic and real data sets. This work established the fundamental building blocks toward a full-fledged geo-stream database management system and has potential impact in many …

The future wireless communication systems are required to meet the growing demands of reliability, bandwidth capacity, and mobility. However, as corruptions such as fading effects, thermal noise, are present in the channel, the occurrence of errors is unavoidable. Motivated by this, the work in this dissertation attempts to improve the system performance by way of exploiting schemes which statistically reduce the error rate, and in turn boost the system throughput. The network can be studied using a simplified model, the two-way relay channel, where two parties exchange messages via the assistance of a relay in between. In such scenarios, this dissertation performs theoretical analysis of the system, and derives closed-form and upper bound expressions of the error probability. These theoretical measurements are potentially helpful references for the practical system design. Additionally, several novel transmission methods including block relaying, permutation modulations for the physical-layer network coding, are proposed and discussed. Numerical simulation results are presented to support the validity of the conclusions.

Location-based services (LBS) are available on a variety of mobile platforms like cell phones, PDA's, etc. and an increasing number of users subscribe to and use these services. Two of the popular models of information flow in LBS are the client-server model and the peer-to-peer model, in both of which, existing approaches do not always provide privacy for all parties concerned. In this work, I study the feasibility of applying cryptographic protocols to design privacy-preserving solutions for LBS from an experimental and theoretical standpoint. In the client-server model, I construct a two-phase framework for processing nearest neighbor queries using combinations of cryptographic protocols such as oblivious transfer and private information retrieval. In the peer-to-peer model, I present privacy preserving solutions for processing group nearest neighbor queries in the semi-honest and dishonest adversarial models. I apply concepts from secure multi-party computation to realize our constructions and also leverage the capabilities of trusted computing technology, specifically TPM chips. My solution for the dishonest adversarial model is also of independent cryptographic interest. I prove my constructions secure under standard cryptographic assumptions and design experiments for testing the feasibility or practicability of our constructions and benchmark key operations. My experiments show that the proposed …

The major challenges facing resource constraint wireless devices are error resilience, security and speed. Three joint schemes are presented in this research which could be broadly divided into error correction based and cipher based. The error correction based ciphers take advantage of the properties of LDPC codes and Nordstrom Robinson code. A cipher-based cryptosystem is also presented in this research. The complexity of this scheme is reduced compared to conventional schemes. The securities of the ciphers are analyzed against known-plaintext and chosen-plaintext attacks and are found to be secure. Randomization test was also conducted on these schemes and the results are presented. For the proof of concept, the schemes were implemented in software and hardware and these shows a reduction in hardware usage compared to conventional schemes. As a result, joint schemes for error correction and security provide security to the physical layer of wireless communication systems, a layer in the protocol stack where currently little or no security is implemented. In this physical layer security approach, the properties of powerful error correcting codes are exploited to deliver reliability to the intended parties, high security against eavesdroppers and efficiency in communication system. The notion of a highly secure and reliable …

While pragmatics, through its integration of situational awareness and real world relevant knowledge, offers a high level of analysis that is suitable for real interpretation of natural dialogue, semantics, on the other end, represents a lower yet more tractable and affordable linguistic level of analysis using current technologies. Generally, the understanding of semantic meaning in literature has revolved around the famous quote ``You shall know a word by the company it keeps''. In this thesis we investigate the role of context constituents in decoding the semantic meaning of the engulfing context; specifically we probe the role of salient concepts, defined as content-bearing expressions which afford encyclopedic definitions, as a suitable source of semantic clues to an unambiguous interpretation of context. Furthermore, we integrate this world knowledge in building a new and robust unsupervised semantic model and apply it to entail semantic relatedness between textual pairs, whether they are words, sentences or paragraphs. Moreover, we explore the abstraction of semantics across languages and utilize our findings into building a novel multi-lingual semantic relatedness model exploiting information acquired from various languages. We demonstrate the effectiveness and the superiority of our mono-lingual and multi-lingual models through a comprehensive set of evaluations on specialized …